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We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
A distributed storage system (DSS) needs to be efficiently accessible and repairable. Recently, considerable effort has been made towards the latter, while the former is usually not considered, since a trivial solution exists in the form of…
DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing…
Heterogeneous Distributed Storage Systems (DSSs) are close to the real world applications for data storage. Each node of the considered DSS, may store different number of packets and each having different repair bandwidth with uniform…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Exponential increase of data has motivated advances of data storage technologies. As a promising storage media, DeoxyriboNucleic Acid (DNA) storage provides a much higher data density and superior durability, compared with state-of-the-art…
Coding for distributed storage gives rise to a new set of problems in coding theory related to the need of reducing inter-node communication in the system. A large number of recent papers addressed the problem of optimizing the total amount…
It has been shown that maximum distance profile (MDP) convolutional codes have optimal recovery rate for windows of a certain length, when transmitting over an erasure channel. In addition, the subclass of complete MDP convolutional codes…
In this paper, we identify a fundamental algorithmic problem that we term succinct dynamic covering (SDC), arising in many modern-day web applications, including ad-serving and online recommendation systems in eBay and Netflix. Roughly…
This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…
The exponentially increasing demand for data storage has been facing more and more challenges during the past years. The energy costs that it represents are also increasing, and the availability of the storage hardware is not able to follow…
It is well known that an (n,k) code can be used to store 'k' units of information in 'n' unit-capacity disks of a distributed data storage system. If the code used is maximum distance separable (MDS), then the system can tolerate any (n-k)…
Maximum-distance-separable (MDS) codes are a class of erasure codes that are widely adopted to enhance the reliability of distributed storage systems (DSS). In (n, k) MDS coded DSS, the original data are stored into n distributed nodes in…
Diffraction drastically limits the bit density in optical data storage. To increase the storage density, alternative strategies involving supplementary recording dimensions and robust read-out schemes must be explored. Here, we propose to…
The double digest problem is a common NP-hard approach to constructing physical maps of DNA sequences. This paper presents a new approach called the enhanced double digest problem. Although this new problem is also NP-hard, it can be solved…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
The monotone minimal perfect hash function (MMPHF) problem is the following indexing problem. Given a set $S= \{s_1,\ldots,s_n\}$ of $n$ distinct keys from a universe $U$ of size $u$, create a data structure $DS$ that answers the following…
Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are…
Data compression is a well-studied (and well-solved) problem in the setup of long coding blocks. But important emerging applications need to compress data to memory words of small fixed widths. This new setup is the subject of this paper.…